Changes between Version 8 and Version 9 of SOPs/vcf_manipulation


Ignore:
Timestamp:
01/05/16 14:16:00 (9 years ago)
Author:
gbell
Comment:

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  • SOPs/vcf_manipulation

    v8 v9  
    8181java -jar /usr/local/gatk/GenomeAnalysisTK.jar -T ValidateVariants -R /path/to/indexed/genome --variant:VCF SNPs.vcf
    8282}}}
     83
     84Convert from VCF to bed (using the [http://bedops.readthedocs.org BEDOPS] toolkit):
     85{{{
     86vcf2bed < my_variants.vcf > my_variants.bed
     87}}}